Gene expression changes in human mesenchymal stem cells from patients with osteoporosis

The aim of the present study was to investigate the underlying molecular mechanisms of osteoporosis and to identify novel candidate genes involved in this disease. The gene expression profile of GSE35958 was downloaded from Gene Expression Omnibus, including five samples of human mesenchymal stem cells from patients with osteoporosis and four control samples. Differentially expressed genes (DEGs) were initially identified following an analysis using Student's t-test. Subsequently, a protein-protein interaction (PPI) network of the significant pathways was constructed, based on the Human Protein Reference Database. In the significant pathways, DEGs were screened using cut-off criteria of FDR<0.1 and |log(2)FC|>1.5. A co-change network for pathways was also constructed using the method of cumulative hypergeometric probability distribution. Finally, the transcriptional regulatory network for DEGs was constructed based on the TRANSFAC database. In total, 1,127 DEGs, including 554 upregulated and 573 downregulated DEGs, were screened. The constructed PPI network for the DEGs involved in the two significant pathways, including focal adhesion and lysosome, demonstrated that the five DEGs with a high degree (>60) were -catenin, SHC-transforming protein 1, RAC- serine/threonine-protein kinase, caveolin 1 and filamin A, with degrees of 135, 117, 117, 73 and 63, respectively. The pathway with the degree of 22 in the constructed co-change network was neuroactive ligand receptor interaction. The nine genes with a high (9) degree in the constructed transcriptional regulatory network were REL-associated protein, upstream stimulatory factor 1, specificity protein 1, Fos-related antigen 1, cyclin-dependent kinase inhibitor 1A, upstream stimulatory factor 2, ETS domain-containing protein Elk-1, JUND and retinoic acid receptor , with degrees of 29, 27, 19, 18, 17, 13, 11, 11 and 9, respectively. The DEGs with high degree in the PPI and transcriptional regulatory networks may be candidate target molecules, which may be used to monitor, diagnose and treat osteoporosis.